AMBER Archive (2008)

Subject: Re: AMBER: D2O

From: Chih-Ying Lin (chihying_at_usc.edu)
Date: Thu Sep 11 2008 - 19:51:03 CDT

Hi
The experiment observes the micelle in D2O solution.
And. there is no other experiments done in H2O solution.

and, I am going to simulate it..... and those are all I know.
Lin

----- Original Message -----
From: Adrian Roitberg <roitberg_at_qtp.ufl.edu>
Date: Thursday, September 11, 2008 9:10 am
Subject: Re: AMBER: D2O
To: amber_at_scripps.edu

> Let's see if I can help.
>
> Indeed, you 'can' use amber from a technical point of view. This
> would
> require a very slight amount of work, changing the mass of the H
> atoms
> in water in the prmtop from 1 to 2.
>
> This will give a very small different final density, but I do not
> believe this would even be really measurable above errors bars.
>
> Besides that, I seriously question the 'need' or 'wisdom' in doing
> such
> simulations !
>
> If you are looking at H exchange from deuterated waters, NO
> program will
> help you unless you do the full calculation using fantastically
> good
> quantum mechanics and very long time scales. I do not believe
> anyone has
> done anything remotely like that for more than 5 or 6 water molecules.
>
> If you are looking at ANY other property, then it is unlikely
> there
> would ever be any difference between D2O and H2O, EVER.
>
> Let's think about this:
>
> 1. Under classical mechanics, the mass has NO effect on ANY
> equilibrium
> thermodynamic properties. The mass simply is nowhere to be found
> in a
> proper statistical description of a system.
>
> 2. Quantum mechanics only cares about masses when either a zero
> point
> energy needs to be computed, or tunneling happens. Since Amber
> (and any
> other classical MD program), for the most part, do not deal with
> those
> issues, D2O and H2O would behave EXACTLY the same for any
> equilibrium
> property. Exemptions are using PIMD for tunneling, etc, for those
> are
> for expert use.
>
> 3. Kinetics depends on masses in a non-trivial way. It has to do
> with
> the acceleration relating to mass and force, but then again, rates
> for
> reactions do not really depend on masses (see point 2 for caveats).
>
> To summarize, Amber is neither better not worse than any other
> program
> to do what you want to do, I seriously suggest that you tell us
> exactly
> what you think you can achieve by this simulation and maybe we can
> help you.
>
> Adrian
>
>
> Chih-Ying Lin wrote:
> >
> > I will simulate a system which the solutes embeded in the D2O
> solution.>
> > Am I suggested using Amber package to do so?
> > or, no....
> >
> >
> > Thank you
> > Lin
> >
> > ----- Original Message -----
> > From: Carlos Simmerling <carlos.simmerling_at_gmail.com>
> > Date: Tuesday, September 9, 2008 4:19 pm
> > Subject: Re: AMBER: D2O
> > To: amber_at_scripps.edu
> >
> >> but for what reason? what are you trying to learn?
> >>
> >> On Tue, Sep 9, 2008 at 3:59 PM, Chih-Ying Lin
> <chihying_at_usc.edu>
> >> wrote:>
> >>> solute embeded in the D2O solution, instead of H2O solution
> >>> what is the suggestion for this?
> >>>
> >>> ----- Original Message -----
> >>> From: Carlos Simmerling <carlos.simmerling_at_gmail.com>
> >>> Date: Tuesday, September 9, 2008 11:21 am
> >>> Subject: Re: AMBER: D2O
> >>> To: amber_at_scripps.edu
> >>>
> >>>> it's important to first clarify to yourself and us what
> >> properties of
> >>>> D2O you are trying to reproduce, as compared to H2O. for
> >> example, are
> >>>> you looking at H/D exchange rates in NMR, or perhaps
> enzymatic
> >> KIE, or
> >>>> something else? each of these would require a different
> approach
> >> (if>> they are even tractable at all)
> >>>> On Tue, Sep 9, 2008 at 1:00 PM, Chih-Ying Lin <chihying_at_usc.edu>
> >>>> wrote:>
> >>>>> Hi
> >>>>> Does amber support D2O simulation?
> >>>>> What is the difference between H2O simulation and D2O
> simulation?>>>>>
> >>>>> And, how about the force field paramters of D2O?
> >>>>>
> >>>>> How to simulate the D2O system instead of H2O?
> >>>>>
> >>>>> Thank you
> >>>>> Lin
> >>>>> -------------------------------------------------------------
> --
> >> ---
> >>>> -----
> >>>>> The AMBER Mail Reflector
> >>>>> To post, send mail to amber_at_scripps.edu
> >>>>> To unsubscribe, send "unsubscribe amber" (in the *body* of the
> >>>> email)> to majordomo_at_scripps.edu
> >>>> --------------------------------------------------------------
> ---
> >> ---
> >>>> ---
> >>>> The AMBER Mail Reflector
> >>>> To post, send mail to amber_at_scripps.edu
> >>>> To unsubscribe, send "unsubscribe amber" (in the *body* of
> the
> >> email)>> to majordomo_at_scripps.edu
> >>> ---------------------------------------------------------------
> ---
> >> -----
> >>> The AMBER Mail Reflector
> >>> To post, send mail to amber_at_scripps.edu
> >>> To unsubscribe, send "unsubscribe amber" (in the *body* of the
> >> email)> to majordomo_at_scripps.edu
> >>
> >>
> >> --
> >> ===================================================================
> >> Carlos L. Simmerling, Ph.D.
> >> Associate Professor Phone: (631) 632-1336
> >> Center for Structural Biology Fax: (631) 632-1555
> >> CMM Bldg, Room G80
> >> Stony Brook University E-mail: carlos.simmerling_at_gmail.com
> >> Stony Brook, NY 11794-5115 Web: http://comp.chem.sunysb.edu
> >> ===================================================================
> >> ----------------------------------------------------------------
> ----
> >> ---
> >> The AMBER Mail Reflector
> >> To post, send mail to amber_at_scripps.edu
> >> To unsubscribe, send "unsubscribe amber" (in the *body* of the
> email)>> to majordomo_at_scripps.edu
> >>
> > -----------------------------------------------------------------
> ------
> > The AMBER Mail Reflector
> > To post, send mail to amber_at_scripps.edu
> > To unsubscribe, send "unsubscribe amber" (in the *body* of the
> email)> to majordomo_at_scripps.edu
> >
>
> --
> Dr. Adrian E. Roitberg
> Associate Professor
> Quantum Theory Project
> Department of Chemistry
>
> Senior Editor. Journal of Physical Chemistry
> American Chemical Society
>
> University of Florida PHONE 352 392-6972
> P.O. Box 118435 FAX 352 392-8722
> Gainesville, FL 32611-8435 Email adrian_at_qtp.ufl.edu
> -------------------------------------------------------------------
> ----
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
> to majordomo_at_scripps.edu
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu